As a commander of your very own naval force you have a fleet to equip and order around. To begin with you will have a good standard fleet which will hopefully take you through the first two missions.
The second mission is already a significant leap up in difficulty compared to the first, but you should be able to manage with the standard fleet in a few tries.
When it is time to start equipping your ships there are some things that could be good to keep in mind.

Point capacity

As you progress you will be allowed a larger and better equipped fleet. How much ‘space’ you currently have at your disposal can be viewed in the ‘Edit Fleet’ menu, at the top. Each ship, weapon and upgrade is worth a specified amount of points, and you can add on as much as you like until your point quota is met. There is however one more limitation. Each ship will have an ‘arms’ cap which is displayed over each individual ship. The scout ship for example has room for 4 different arms.

You are able to remove and add ships and equipment freely. Your ‘currency’ is entirely re-usable. So if you purchase a ship for 700 points and change your mind, you can always click the “Remove the ship” button and all points will be available again. So feel free to equip and discard as you please until you find a setup that you like.

Equipping the ship

In the fleet editor you can click on a specific ship to equip it. ‘Hull Sections’ contain upgrades to your hull while the Armament section allows for you to purchase weapons to mount on the ship. As explained in the bottom left of your screen, yellow spots are for Offensive items, blue is for defensive and green are for either.

Some weapons require more than one square to fit, but this is fairly straight forward and you should realize quite soon what goes where. To equip/remove something, simply drag and drop it on and off your boat.

Keep in mind in what direction the gun is aimed. A gun pointing to your port side will only be able to fire in that direction. For some missions it may be viable to only equip a ship to shoot in one direction. This is something you will come to realize on your own when you should be doing it. I will not tell you when, but just inform you that it may be needed in some situations.

Naming your ship

And last, you need to give your new addition to the fleet a suitable name for your ship. This you do in the top most left, where by default the ship class will be entered as a name. Let your creativity flow and give your ship a more suitable label.

Saving your ship design

If you designed yourself an awesome boat but you don’t need it for this particular mission. Then you can save your ships blueprint by clicking “Save a blueprint of this ship” in the top right corner. This allows you to quickly add on that particular ship to your fleet in later missions.

Editing your pre-defined fleets for multiplayer

In the shipyard from the main menu you can create fleets with different compositions and save them for repeated use and quick switching.

Basic tips (my own opinion and experience, might not suit you)

When editing your fleet. Make sure you have a setup that can deal with opponents in different situations. Having no guns that can fire on short range can be a problem if you run into an enemy fleet that speeds up next to you. Do you have cover to all sides, or is your fleet requiring a special formation to cover all angles? Artillery is not so good unless you have a spotter as the range is much greater than the average sight range of a ship!

You will have to repeat many missions over and over. I recommend that you experiment a lot with the various weapons and equipment, making adjustments to compensate where you failed in the previous attempt.